8Y6V | pdb_00008y6v

Near-atomic structure of icosahedrally averaged jumbo bacteriophage PhiKZ capsid


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Capsid structure of bacteriophage Phi KZ provides insights into assembly and stabilization of jumbo phages.

Yang, Y.Shao, Q.Guo, M.Han, L.Zhao, X.Wang, A.Li, X.Wang, B.Pan, J.A.Chen, Z.Fokine, A.Sun, L.Fang, Q.

(2024) Nat Commun 15: 6551-6551

  • DOI: https://doi.org/10.1038/s41467-024-50811-1
  • Primary Citation of Related Structures:  
    8Y6V

  • PubMed Abstract: 

    Jumbo phages are a group of tailed bacteriophages with large genomes and capsids. As a prototype of jumbo phage, ΦKZ infects Pseudomonas aeruginosa, a multi-drug-resistant (MDR) opportunistic pathogen leading to acute or chronic infection in immunocompromised individuals. It holds potential to be used as an antimicrobial agent and as a model for uncovering basic phage biology. Although previous low-resolution structural studies have indicated that jumbo phages may have more complicated capsid structures than smaller phages such as HK97, the detailed structures and the assembly mechanism of their capsids remain largely unknown. Here, we report a 3.5-Å-resolution cryo-EM structure of the ΦKZ capsid. The structure unveiled ten minor capsid proteins, with some decorating the outer surface of the capsid and the others forming a complex network attached to the capsid's inner surface. This network seems to play roles in driving capsid assembly and capsid stabilization. Similar mechanisms of capsid assembly and stabilization are probably employed by many other jumbo viruses.


  • Organizational Affiliation
    • School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
gp28A [auth D]320Phikzvirus phiKZMutation(s): 0 
UniProt
Find proteins for Q8SDD4 (Pseudomonas phage phiKZ)
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Go to UniProtKB:  Q8SDD4
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UniProt GroupQ8SDD4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
gp35271Phikzvirus phiKZMutation(s): 0 
UniProt
Find proteins for Q8SDC7 (Pseudomonas phage phiKZ)
Explore Q8SDC7 
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UniProt GroupQ8SDC7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
gp85C [auth E],
D [auth F]
149Phikzvirus phiKZMutation(s): 0 
UniProt
Find proteins for Q8SD77 (Pseudomonas phage phiKZ)
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UniProt GroupQ8SD77
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
gp86E [auth G]428Phikzvirus phiKZMutation(s): 0 
UniProt
Find proteins for Q8SD76 (Pseudomonas phage phiKZ)
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UniProt GroupQ8SD76
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
gp91F [auth H]181Phikzvirus phiKZMutation(s): 0 
UniProt
Find proteins for Q8SD71 (Pseudomonas phage phiKZ)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
gp93G [auth K],
H [auth L],
I [auth M]
435Phikzvirus phiKZMutation(s): 0 
UniProt
Find proteins for Q8SD69 (Pseudomonas phage phiKZ)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
gp119177Phikzvirus phiKZMutation(s): 0 
UniProt
Find proteins for Q8SD43 (Pseudomonas phage phiKZ)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
gp120747Phikzvirus phiKZMutation(s): 0 
UniProt
Find proteins for Q8SD42 (Pseudomonas phage phiKZ)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
gp162LA [auth N],
MA [auth O],
NA [auth P]
522Phikzvirus phiKZMutation(s): 0 
UniProt
Find proteins for Q8SD00 (Pseudomonas phage phiKZ)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
gp184OA [auth I]230Phikzvirus phiKZMutation(s): 0 
UniProt
Find proteins for Q8SCX8 (Pseudomonas phage phiKZ)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
gp244PA [auth C]118Phikzvirus phiKZMutation(s): 0 
UniProt
Find proteins for Q8SCR8 (Pseudomonas phage phiKZ)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2021YFC2302500
Shenzhen Medical Research FundChinaD2301008
Shenzhen Science and Technology ProgramChinaZDSYS20230626091203007
R&D Program of Guangzhou LaboratoryChinaSRPG22-003

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release